As the tenth anniversary of 9/11 approaches, the unexpected extent of the damage Americans have done to themselves and their institutions is coming into better focus. The event that “changed everything” did turn out to change Washington in ways more startling than most people realize. On terrorism and national security, to take an obvious (if seldom commented upon) example, the confidence of the US government seems to have been severely, perhaps irreparably, shaken when it comes to that basic and essential American institution: the courts.

If, in fact, we are a “nation of laws,” you wouldn’t know it from Washington’s actions over the past few years. Nothing spoke more strikingly to that loss of faith, to our country’s increasing incapacity for meeting violence with the law, than the widely hailed decision to kill rather than capture Osama bin Laden.

Clearly, a key factor in that decision was a growing belief, widely shared within the national-security establishment, that none of our traditional or even newly created tribunals, civilian or military, could have handled a bin Laden trial. Washington’s faith went solely to Navy SEALs zooming into another country’s sovereign airspace on a moonless night on a mission to assassinate bin Laden, whether he offered the slightest resistance or not. It evidently seemed so much easier to the top officials overseeing the operation—and so much less messy—than bringing a confessed mass murderer into a courtroom in, or even anywhere near, the United States.

The decision to kill bin Laden on sight rather than capture him and bring him to trial followed hard on the heels of an ignominious Obama administration climb-down on its plan to try the “mastermind” of the 9/11 attacks, Khalid Sheikh Mohammed, or KSM, in a federal court in New York City. Captured in Pakistan in May 2003 and transferred to Guantánamo in 2006, his proposed trial was, under political pressure, returned to a military venue earlier this year.

Given the extraordinary record of underperformance by the military commissions system—only six convictions in ten years—it’s hard to escape the conclusion that the United States has little faith in its ability to put on trial a man assumedly responsible for murdering thousands.

And don’t assume that these high-level examples of avoiding the court system are just knotty exceptions that prove the rule. There is evidence that the administration’s skepticism and faint-heartedness when it comes to using the judicial system risks becoming pervasive.

Pushing Guilt Before Trial

Needless to say, this backing away from courts of law as institutions appropriate for handling terrorism suspects began in the Bush-Cheney years. Top officials in the Bush administration believed civilian courts to be far too weak for the “Global War on Terror” they had declared. This, as they saw it, was largely because those courts would supposedly gift foreign terrorist suspects with a slew of American legal rights that might act as so many get-out-of-jail-free cards.

As a result, despite a shining record of terrorism convictions in civilian courts in the 1990s—including the prosecutions of those responsible for the 1993 attempt to take down a tower of the World Trade Center—President Bush issued a military order on November 13, 2001, that established the court-less contours of public debate to come. It mandated that non-American terrorists captured abroad would be put under the jurisdiction of the Pentagon, not the federal court system. This was “war,” after all, and the enemy had to be confronted by fighting men, not those sticklers for due process, civilian judges and juries.

The federal courts have, of course, continued to try American citizens and residents (and even, in a few cases, individuals captured abroad) in terror cases of all sorts—with an 87 percent conviction rate for both violent and nonviolent crimes. In fact, 2010 was a banner year for terrorism prosecutions when it came to American citizens and residents, and 2011 is following suit. As could have been predicted, in the vast majority of these cases—all the ones that mattered—there were convictions.

You might think, then, that the courts had proved their mettle against mounting criticism and distrust of a system said to be insufficiently harsh. And initially, Obama’s Department of Justice defended civilian courts as resilient and flexible enough to try terror cases.

But that didn’t last. Recently, the Obama administration has reinforced a policy (begun under President Bush) which offers an ominous new twist on American justice: punishment before trial. It has, for example, relied upon various extreme methods of pre-trial isolation—including a version of restrictive orders known as Special Administrative Measures, or SAMs—that reek of punitiveness and have often caused severe psychological deterioration in suspects awaiting trial on terrorism charges. The most noteworthy case of this is Syed Fahad Hashmi’s. An American citizen arrested while studying in England, Hashmi had allowed an acquaintance, Mohammed Junaid Babar, to stay in his apartment for two weeks. Babar, who testified against Hashmi and was later released, allegedly had socks, ponchos, and raingear intended for Al Qaeda in his luggage and allegedly used Hashmi’s cell phone to call terrorist conspirators. Hashmi, accused of “material support” for Al Qaeda, was kept under SAMs for three years without trial—until he finally pled guilty.

The urge to punish before a verdict comes in reflects the same deep-seated conviction that the US court system is simply not to be trusted to do its job. Two recent cases—that of whistleblowers Thomas Drake and Bradley Manning—illustrate how, in cases where national security is believed to be at stake, Obama-era pre-trial treatment has taken up the distrust of the courts, civilian or military, that characterized the Bush years.

Drake, an executive for the National Security Agency (NSA), became a whistleblower over what he considered mistaken policy decisions about an ill-performing data-sifting program which, among other things, he thought squandered taxpayer money. Subsequently, he revealed his disagreement with the agency’s warrantless wire-tapping program, which he believed overstepped legal boundaries. Charged initially with violating the Espionage Act and threatened with a draconian thirty-five-year jail sentence, Drake finally pled this past June to a misdemeanor count of “exceeding the authorized use of a government computer.”

In Drake’s four-year saga, his pre-punishment took the form not of pre-trial detention but of the destruction of his livelihood. He was initially fired from the NSA and from the National Defense University position to which the NSA had assigned him. Once indicted in 2010, he was forced to resign from a subsequent teaching post at Strayer University. All told, the formal and informal hounding of Drake resulted in the loss of his jobs and pension, as well as $82,000 in legal costs. Ultimately, Drake was sentenced to a year’s probation and 240 hours of mandatory community service. By that time, he had been ruined financially and professionally, thanks to the government’s disparagement of him and the multi-year delay between its accusations and the lodging of formal charges against him. Drake now works at an Apple Store. In other words, well before the government took its chances in court, Thomas Drake was punished.

Another highly publicized case where punishment preceded trial has been the mistreatment of Army Private Bradley Manning while in military custody in a Marine brig in Quantico, Virginia, awaiting charges. The Obama administration believes he turned over a trove of secret military and State Department documents to the website WikiLeaks. Following his arrest, Manning was kept in subhuman conditions. He was forced to sleep naked and to strip for daily inspections, though as news about his situation generated bad publicity, he was eventually allowed to sleep in a “tear-proof” gown.

There is something deeply disturbing about the very different ways Manning and Drake were pre-punished by the government—both directly in the case of Manning and indirectly in the case of Drake—before being given due process of any kind. Like bin Laden’s killing, both cases reflect an unspoken worry in Washington that our courts will prove insufficiently ruthless and so incapable of giving the “obviously guilty” what they “obviously” deserve.

The Courts Take Notice

As it turns out, the judicial system hasn’t taken the government’s new attitude lying down. Various judges and juries have, in fact, shown themselves to be unfazed by both public and governmental pressures and have, in terror and national security cases, demonstrated signs of balance and of a concern for justice, rather than being driven by a blind sense of revenge.

In the past year, there has been an unprecedented number of high-profile terrorism trials. All have resulted in convictions, which have nonetheless not reflected the unstinting harshness that critics of court-centered counterterrorism insist upon. In the case of Ahmed Ghailani, the sole Guantánamo detainee to face trial in the nation’s criminal justice system, the jury, having done its work of assessing the evidence, acquitted the defendant on 284 of 285 counts, including all the murder charges associated with the 1998 bombings of the US embassies in Kenya and Tanzania. On the single count on which he was convicted, however, Ghailani was given a life sentence without parole.

Meanwhile, a high-profile terrorism case—that of Tagawwur Rana—ended in a jury acquittal on its most serious charge. Rana had been accused of cooperating in the 2008 terrorist attacks in Mumbai, India, which resulted in the deaths of more than 160 individuals. The jury found Rana guilty of material support, but not of helping to coordinate the attack.

These cases and others like them have, of course, been fodder for all the usual critics who consider anything but a 100 percent conviction rate on all charges in all cases to be a sure sign not of the justice system’s strength but of its fundamental weakness. And yet, such cases have showcased just how effectively the system still works, in a more nuanced way than in the previous near-decade, as well as in a subtler and more just way than Washington has managed to approximate over that same period. Despite the fears, pressures, and scare tactics that are entangled with all such terror cases, we now have living proof that juries can think for themselves, and guilt can be a partial matter, rather than a Washington slam-dunk.

Of late, federal judges on such cases also seem to have been signaling to the government’s representatives that they must be more restrained in their approach to national security cases, both in and out of court. In late June, for instance, during the sentencing of three of the men convicted of conspiring to bomb two synagogues in Riverdale, New York, and to launch a Stinger missile aimed at aircraft over Newburgh’s Air National Guard Base, Judge Colleen McMahon struck back at the government’s case. “I believe beyond a shadow of a doubt,” she said, “that there would have been no crime here except the government instigated it, planned it, and brought it to fruition. That does not mean that there was no crime. The jury concluded that you were not entrapped, and I see no basis to overturn their verdict.”

In the Drake case, Judge Richard Bennett was similarly distraught about the evident excesses in the government’s approach. At sentencing for the single minor count to which Drake agreed to plead, the judge bluntly refused to impose the $50,000 fine the prosecution was pushing for on the grounds that punishment had already been administered—prior to the court process. “There has been financial devastation wrought upon this defendant,” said Bennett, “that far exceeds any fine that can be imposed by me. And I’m not going to add to that in any way. And it’s very obvious to me in terms of some of the irritation I’ve expressed…not only my concern over the delay in this case…[but also the prosecution’s] inability to explain…the delay in this case.… I think that somebody somewhere in the US government has to say…that the American public deserves better than this."

In the recent jury decisions, as in the growing expressions of judicial dissatisfaction, an optimist might find signs that the system is finally starting to right itself. On the other hand, a pessimist might come to the conclusion that the government will, in the future, simply put even more energy into avoiding the court system.

The bottom line is that the Obama administration, like its predecessor, defines success in terrorism prosecutions not by assessing whether or not due process and fair verdicts are administered, but solely in terms of what they deem proper punishment for those accused of violating national security—especially when doing so minimizes partisan political clashes. By refusing to rein in its evident distrust of the judicial system when it comes to national security, the government is perpetuating a legal landscape that, to this day, lies in the shadow of Osama bin Laden.